He served as a United States Indian agent for a period beginning in 1822 in Michigan, where he married Jane Johnston, mixed-race daughter of a prominent Scotch-Irish fur trader and Ojibwa mother, herself a daughter of Ojibwa war chief Waubojeeg. She taught him the Ojibwe language and much about her maternal culture. They had several children, two of whom survived past childhood. She is now recognized as the first Native American literary writer in the United States.

In 1846 the widower Schoolcraft was commissioned by Congress for a major study, known as Indian Tribes of the United States, which was published in six volumes from 1851 to 1857. He married again in 1847, to Mary Howard, from a slaveholding family in South Carolina. In 1860 she published the bestselling The Black Gauntlet, an anti-Uncle Tom's Cabin novel.

His father was a glassmaker, and Henry initially studied and worked in the same industry. Schoolcraft wrote his first paper on the topic, Vitreology (1817). After working in several glass works in New York, Vermont and New Hampshire, the young Schoolcraft left the family business at age 25 to explore the western frontier.

From November 18 to February 1819, Schoolcraft and his companion Levi Pettibone made an expedition from Potosi, Missouri, to what is now Springfield. They traveled further down the White River into Arkansas, making a survey of the geography, geology, and mineralogy of the area. Schoolcraft published this study in A View of the Lead Mines of Missouri (1819). In this book he correctly identified the potential for lead deposits in the region; Missouri eventually became the number one lead-producing state. (French colonists had a lead mine outside St. Louis developed in the 18th century.) He also published Journal of a Tour into the Interior of Missouri and Arkansaw (1821), the first written account of an exploration of the Ozarks.

This expedition and his resulting publications brought Schoolcraft to the attention of the Secretary of War, John C. Calhoun, who saw him as "a man of industry, ambition, and insatiable curiosity."[1] Calhoun recommended him to the Michigan Territorial Governor, Lewis Cass, for a position on an expedition led by Cass to explore the wilderness region of Lake Superior and the lands west to the Mississippi River. Beginning in the spring of 1820, Schoolcraft served as a geologist on the Lewis Cass expedition. Beginning in Detroit, they traveled nearly 2,000 miles (3,200 km) along Lake Huron and Lake Superior, west to the Mississippi River, down the river to present-day Iowa, and then returning to Detroit after tracing the shores of Lake Michigan.

The expedition was intended to establish the source of the Mississippi River, and in part to settle the question of an undetermined boundary between the United States and BritishCanada. The expedition traveled as far upstream as Upper Red Cedar Lake in present-day Minnesota. Since low water precluded navigating farther upstream, the lake was designated the river's headwaters, and renamed in honor of Cass. (Schoolcraft noted, however, that locals informed the expedition that it was possible to navigate by canoe farther upstream earlier in the year, when water levels were higher.) Schoolcraft's account of the expedition was published as A Narrative Journal of Travels Through the Northwestern Regions...to the Sources of the Mississippi River (1821).

In 1821 he was a member of another government expedition that traveled through Illinois, Indiana and Ohio.

In 1832, he led a second expedition to the headwaters of the Mississippi River. Arriving a month earlier than had the 1820 expedition, he was able to take advantage of higher water to navigate to Lake Itasca.

Schoolcraft met his first wife soon after being assigned in 1822 to Sault Ste. Marie, Michigan, as its first US Indian agent. Two years before, the government had built Fort Brady and wanted to establish an official presence to forestall any renewed British threat following the War of 1812. The government tried to ensure against British agitation of the Ojibwe.

Jane was also known as Bamewawagezhikaquay (Woman of the Sound the Stars Make Rushing Through the Sky). Her knowledge of the Ojibwe language and legends, which she shared with Schoolcraft, formed in part the source material for Longfellow's epic poem The Song of Hiawatha.[3]

Jane and Henry had four children together:

William Henry (b. June 1824—d. March 1827) died of croup at nearly three.[4] Jane Schoolcraft wrote poems expressing her grief about his loss.[5]

The Schoolcrafts sent Janee and John to a boarding school in Detroit for part of their education. Janee at 11 could handle the transition, but John at nine had a more difficult time and missed his parents.

The Schoolcrafts had a literary marriage, producing a family magazine. They included their own poetry in letters to each other through the years. Jane suffered from frequent illnesses. She died in 1842, while visiting a sister in Canada, and was buried at St. John's Anglican Church, Ancaster, Ontario.[2]

On January 12, 1847, after moving to Washington, DC, Schoolcraft married again, at age 53, to Mary Howard (died March 12, 1878),[6] a southern slaveholder from an elite planter family of the Beaufort district of South Carolina.[7] Her support of slavery and opposition to mixed-race unions created strains in her relationship with the Schoolcraft children.[8] They became alienated from both her and their father.

After Schoolcraft's hands became paralyzed in 1848 from a rheumatic condition, Mary devoted much of her attention to caring for him and helping him complete his massive study of American Indians, which had been commissioned by Congress in 1846.[7]

Schoolcraft created The Muzzeniegun, or Literary Voyager, a family magazine which produced in the winter of 1826–1827 and circulated among friends ("muzzeniegun" being Ojibwe for book). It contained mostly his own writings, although he did include a few pieces from his wife and a few other locals.[11] Although they produced only single issues, each was distributed widely to residents in Sault Ste. Marie, then to Schoolcraft's friends in Detroit, New York, and other eastern cities.[12] Jane Johnston Schoolcraft used the pen names of "Rosa" and Leelinau as personae to write about different aspects of Indian culture.[13]

Schoolcraft was elected to the legislature of the Michigan Territory, where he served from 1828 to 1832. In 1832, he traveled again to the upper reaches of the Mississippi to settle continuing troubles between the Ojibwe and Dakota (Sioux) nations. He reached out to talk to as many Native American leaders as possible to maintain the peace. He was also provided with a surgeon and given instructions to begin vaccinating Indians against smallpox. He determined that smallpox had been unknown among the Ojibwe before the return in 1750 of a war party that had contact with Europeans on the East Coast. They had gone to Montreal to assist the French against the British in the French and Indian War (the North American front of the Seven Years' War).

During the voyage, Schoolcraft took the opportunity to explore the region, making the first accurate map of the Lake District around western Lake Superior. He discovered the true headwaters of the Mississippi River in Lake Itasca, a name which he coined from the Latin words veritas meaning 'truth' and caput meaning 'head'.[14] The nearby Schoolcraft River, the first major tributary of the Mississippi, was later named in his honor. United States newspapers widely covered this expedition. Schoolcraft followed up with a personal account of the discovery with his book, Narrative of an Expedition Through the Upper Mississippi River to Itasca Lake (1834).

After his territory for Indian Affairs was greatly increased in 1833, Schoolcraft and his wife Jane moved to Mackinac Island, the new headquarters of his administration. In 1836, he was instrumental in settling land disputes with the Ojibwe. He worked with them to accomplish the Treaty of Washington (1836), by which they ceded to the United States a vast territory of more than 13 million acres (53,000 km²), worth many millions of dollars. He believed that the Ojibwe would be better off learning to farm and giving up their wide hunting lands. The government agreed to pay subsidies and provide supplies while the Ojibwe made a transition to a new way of living, but its provision of the promised subsidies was often late and underfunded. The Ojibwe suffered as a result.

In 1838 pursuant to the terms of the treaty, Schoolcraft oversaw the construction of the Indian Dormitory on Mackinac Island. The building is listed on the National Register of Historic Places. It provided temporary housing to the Ojibwe who came to Mackinac Island to receive annuities during their transition to what was envisioned by the US government as a more settled way of life.

In 1839 Schoolcraft was appointed Superintendent of Indian Affairs in the Northern Department. He began a series of Native American studies later published as the Algic Researches (2 vols., 1839). These included his collection of Native American stories and legends, many of which his wife Jane Johnston Schoolcraft told him or translated for him from her culture.

While in Michigan, Schoolcraft became a member of the Board of Regents of the University of Michigan in its early years. In this position he helped establish the state university's financial organization.[15]

Schoolcraft founded and contributed to the first United States journal on public education, The Journal of Education. He also published The Souvenir of the Lakes, the first literary magazine in Michigan.[15]

When the Whig Party came to power in 1841 with the election of William Henry Harrison, Schoolcraft lost his political position as Indian agent. He and Jane moved to New York. She died the next year during a visit with a sister in Canada, while Schoolcraft was traveling in Europe.

He continued to write about Native Americans. In 1846 Congress commissioned him to develop a comprehensive reference work on American Indian tribes. Schoolcraft traveled to England to request the services of George Catlin to illustrate his proposed work, as the latter was widely regarded as the premier illustrator of Indian life. Schoolcraft was deeply disappointed when Catlin refused. Schoolcraft later engaged the artist Seth Eastman as illustrator. An Army brigadier general, Eastman was renowned for his paintings of Native American peoples. He had two extended assignments at Fort Snelling in present-day Minnesota, the second time as commander of the fort, and had closely studied, drawn and painted the people of the Indian cultures of the Great Plains.

Schoolcraft worked for years on the history and survey of the Indian tribes of the United States. It was published in six volumes from 1851-1857 by J. B. Lippincott & Co. of Philadelphia. Critics praised its scholarship and valuable content by Schoolcraft, and the meticulous and knowledgeable illustrations by Eastman. Critics also noted the work's shortcomings, including a lack of index, and poor organization, which made the information almost inaccessible. Almost a hundred years later, in 1954, the Bureau of American Ethnology of the Smithsonian Institution prepared and published an index to the volumes. (It was not until 1928 that the US government had another overall study of the conditions of American Indians; it was informally known as the Meriam Report, after the technical director of the team, Lewis Meriam.)

“The Rise of the West, or a Prospect of the Mississippi Valley,” a poem (Detroit, 1827)

“Indian Melodies,” a poem (1830)

The Man of Bronze (1834)

Iosco, or the Vale of Norma (Detroit, 1834)

Narrative of an Expedition Through the Upper Mississippi River to Itasca Lake (New York, 1834)

“Helderbergia, or the Apotheosis of the Heroes of the Anti-Rent War,” an anonymous poem (Albany, 1835)

Algic Researches, a book of Indian allegories and legends (2 vols., 1839)

Cyclopædia indianensis, of which only a single number was issued (1842)

“Alhalla, or the Land of Talladega,” a poem published under the pen-name “Henry Rowe Colcraft” (1843)

Oneota, or Characteristics of the Red Race of America (1844-5) Republished as The Indian and his Wigwam (1848)

Report on Aboriginal Names and the Geographical Terminology of New York (1845)

Plan for Investigating American Ethnology (1846)

Notes on the Iroquois, containing his report on the Six Nations (Albany, 1846; enlarged editions, New York, 1847 and 1848)

The Red Race of America (1847)

Notices of Antique Earthen Vessels from Florida (1847)

Address on Early American History (New York, 1847)

Outlines of the Life and Character of Gen. Lewis Cass (Albany, 1848)

Bibliographical Catalogue of Books, Translations of the Scriptures, and other Publications in the Indian Tongues of the United States (Washington, 1849)

American Indians, their History, Condition, and Prospects (Auburn, 1850)

Personal Memoirs of a Residence of Thirty Years with the Indian Tribes on the American Frontiers, 1812 to 1842 (Philadelphia, 1851)

Historical and Statistical Information respecting the History, Condition, and Prospects of the Indian Tribes of the United States, with illustrations by Capt. Seth Eastman, published by authority of congress, which appropriated nearly $30,000 a volume for the purpose (6 vols., 1851-7) He had collected material for two additional volumes, but the government suddenly suspended the publication of the work.

Scenes and Adventures in the Semi-Alpine Region of the Ozark Mountains of Missouri and Arkansas, a revised edition of his first book of travel (1853)

Summary Narrative of an Exploratory Expedition to the Sources of the Mississippi River in 1820, resumed and completed by the Discovery of its Origin in Itasca Lake in 1832 (1854)

The Myth of Hiawatha, and other Oral Legends (1856).

Mentor L. Williams, ed., Narrative Journal of travels Through the Northwestern Regions of the United States Extending from Detroit through the Great Chain of the American Lakes to the Sources of the Mississippi River in the year 1820, East Lansing, Michigan: The Michigan State College Press, 1953.

The Indian Fairy-Book, from Original Legends (New York, 1855), was compiled from notes that he furnished to the editor, Cornelius Mathews.